contigs_taxonomic_classification

Description¶

Getting per contig taxonomic annotations for metagenomic assembly based on taxonomic classification of predicted proteins with DIAMOND and CAT.

nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install contigs_taxonomic_classification

This subworkflow is used by the following pipelines:

This subworkflow uses the following components:

Name	Type	Description	Pattern
`contigs`	file	The input channel containing file with metagenomic assembly Structure: [ val(meta), path(fasta) ]	`*.{fasta, fasta.gz, fa, fa.gz, fna, fna.gz}`
`proteins`	file	The input channel containing proteins predicted for the given metagenome CAT assumes that predicted proteins have ids in format _ Structure: [ val(meta), path(fasta) ]	`*.{fasta, fasta.gz, fa, fa.gz, faa, faa.gz}`
`cat_db`	path	Directory containing the CAT database produced with catpack/prepare The folder must contain DIAMOND db .dmnd, .fastaid2LCAtaxid, *.taxids_with_multiple_offspring Structure: [ val(meta), path(db_folder) ]	-
`cat_taxonomy_db`	path	Directory containing the tax/ folder of the CAT database produced with catpack/prepare The folder must contain names.dmp and nodes.dmp Structure: [ val(meta), path(tax_db_folder) ]	-

Name	Type	Description	Pattern
`diamond_output`	file	Channel containing a TSV file with matches of predicted proteins to a database Structure: [ val(meta), path(file) ]	`*.{txt, txt.gz}`
`cat_output`	file	Channel containing a TSV file with taxonomic classification of contigs Structure: [ val(meta), path(file) ]	`*.contig2classification.txt`
`krona_html`	file	Channel containing a HTML file with Krona plot of taxonomic classification of contigs Structure: [ val(meta), path(file) ]	`*.html`
`versions`	file	File containing software versions Structure: [ path(versions.yml) ]	`versions.yml`